Y14B_ORYSJ
ID Y14B_ORYSJ Reviewed; 197 AA.
AC Q6ATR0; A0A023T4L4;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2004, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=RNA-binding protein Y14B {ECO:0000305};
DE Short=OsY14b {ECO:0000303|PubMed:24416299};
DE AltName: Full=RNA-binding protein 8A {ECO:0000305};
GN Name=Y14B {ECO:0000303|PubMed:24416299};
GN Synonyms=RBM8 {ECO:0000303|PubMed:24416299};
GN OrderedLocusNames=Os03g0809900 {ECO:0000312|EMBL:BAF13575.1},
GN LOC_Os03g59550 {ECO:0000312|EMBL:ABF99481.1};
GN ORFNames=OSJNBa0028F23.11 {ECO:0000312|EMBL:AAT77901.1};
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND INTERACTION WITH MAGO1 AND MAGO2.
RX PubMed=24416299; DOI=10.1371/journal.pone.0084842;
RA Gong P., Zhao M., He C.;
RT "Slow co-evolution of the MAGO and Y14 protein families is required for the
RT maintenance of their obligate heterodimerization mode.";
RL PLoS ONE 9:E84842-E84842(2014).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16109971; DOI=10.1101/gr.3869505;
RG The rice chromosome 3 sequencing consortium;
RA Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA Jin W., Lee H.R., Jiang J., Jackson S.;
RT "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT and diverged grass species.";
RL Genome Res. 15:1284-1291(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [5]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
RN [7]
RP FUNCTION, AND INTERACTION WITH MAGO1 AND MAGO2.
RX PubMed=25230811; DOI=10.1111/tpj.12672;
RA Gong P., Quan H., He C.;
RT "Targeting MAGO proteins with a peptide aptamer reinforces their essential
RT roles in multiple rice developmental pathways.";
RL Plant J. 80:905-914(2014).
RN [8]
RP FUNCTION, INTERACTION WITH MAGO1 AND MAGO2, SUBCELLULAR LOCATION, AND
RP INDUCTION.
RX PubMed=24820023; DOI=10.1104/pp.114.237958;
RA Gong P., He C.;
RT "Uncovering divergence of rice exon junction complex core heterodimer gene
RT duplication reveals their essential role in growth, development, and
RT reproduction.";
RL Plant Physiol. 165:1047-1061(2014).
RN [9]
RP INTERACTION WITH EIF4A3/RH2 AND RH34.
RX PubMed=27071313; DOI=10.1186/s12870-016-0769-5;
RA Huang C.K., Sie Y.S., Chen Y.F., Huang T.S., Lu C.A.;
RT "Two highly similar DEAD box proteins, OsRH2 and OsRH34, homologous to
RT eukaryotic initiation factor 4AIII, play roles of the exon junction complex
RT in regulating growth and development in rice.";
RL BMC Plant Biol. 16:84-84(2016).
CC -!- FUNCTION: Core component of the splicing-dependent multiprotein exon
CC junction complex (EJC) deposited at splice junctions on mRNAs. The EJC
CC is a dynamic structure consisting of core proteins and several
CC peripheral nuclear and cytoplasmic associated factors that join the
CC complex only transiently either during EJC assembly or during
CC subsequent mRNA metabolism. The EJC marks the position of the exon-exon
CC junction in the mature mRNA for the gene expression machinery and the
CC core components remain bound to spliced mRNAs throughout all stages of
CC mRNA metabolism thereby influencing downstream processes including
CC nuclear mRNA export, subcellular mRNA localization, translation
CC efficiency and nonsense-mediated mRNA decay (NMD). The MAGO-Y14
CC heterodimer inhibits the ATPase activity of EIF4A3, thereby trapping
CC the ATP-bound EJC core onto spliced mRNA in a stable conformation. The
CC MAGO-Y14 heterodimer interacts with the EJC key regulator PYM leading
CC to EJC disassembly in the cytoplasm (By similarity). EJC core
CC heterodimers play essential roles in plant growth and development, and
CC pollen and seed development (PubMed:25230811, PubMed:24820023). The
CC MAGO-Y14 heterodimer selectively binds to the UDT1 (UNDEVELOPED TAPETUM
CC 1) pre-mRNA transcript and regulates the splicing of UDT1, a key
CC regulator in stamen development (PubMed:24820023).
CC {ECO:0000250|UniProtKB:Q9Y5S9, ECO:0000269|PubMed:24820023,
CC ECO:0000269|PubMed:25230811}.
CC -!- SUBUNIT: Heterodimers with MAGO1 and MAGO2 (PubMed:24416299,
CC PubMed:25230811, PubMed:24820023). Interacts with EIF4A3/RH2 and RH34
CC (PubMed:27071313). Part of the mRNA splicing-dependent exon junction
CC complex (EJC); the core complex contains MLN51/CASC3, EIF4A3, MAGO and
CC Y14 (Probable). {ECO:0000269|PubMed:24416299,
CC ECO:0000269|PubMed:24820023, ECO:0000269|PubMed:25230811,
CC ECO:0000269|PubMed:27071313, ECO:0000305|PubMed:24416299}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:24820023}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q9Y5S9}. Note=Nucleocytoplasmic shuttling
CC protein. Travels to the cytoplasm as part of the exon junction complex
CC (EJC) bound to mRNA. {ECO:0000250|UniProtKB:Q9Y5S9}.
CC -!- SIMILARITY: Belongs to the RBM8A family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AHX83803.1; Type=Miscellaneous discrepancy; Note=Sequencing errors.; Evidence={ECO:0000305};
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DR EMBL; KF051017; AHX83803.1; ALT_SEQ; mRNA.
DR EMBL; AC135595; AAT77901.1; -; Genomic_DNA.
DR EMBL; DP000009; ABF99481.1; -; Genomic_DNA.
DR EMBL; AP008209; BAF13575.1; -; Genomic_DNA.
DR EMBL; AP014959; BAS86989.1; -; Genomic_DNA.
DR EMBL; AK103277; -; NOT_ANNOTATED_CDS; mRNA.
DR RefSeq; XP_015632650.1; XM_015777164.1.
DR AlphaFoldDB; Q6ATR0; -.
DR SMR; Q6ATR0; -.
DR STRING; 4530.OS03T0809900-01; -.
DR PaxDb; Q6ATR0; -.
DR PRIDE; Q6ATR0; -.
DR EnsemblPlants; Os03t0809900-01; Os03t0809900-01; Os03g0809900.
DR GeneID; 4334528; -.
DR Gramene; Os03t0809900-01; Os03t0809900-01; Os03g0809900.
DR KEGG; osa:4334528; -.
DR eggNOG; KOG0130; Eukaryota.
DR HOGENOM; CLU_012062_18_1_1; -.
DR InParanoid; Q6ATR0; -.
DR OMA; ESIPFAG; -.
DR OrthoDB; 1444995at2759; -.
DR Proteomes; UP000000763; Chromosome 3.
DR Proteomes; UP000059680; Chromosome 3.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0035145; C:exon-exon junction complex; IBA:GO_Central.
DR GO; GO:0003729; F:mRNA binding; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0051028; P:mRNA transport; IEA:UniProtKB-KW.
DR GO; GO:0000184; P:nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; IEA:UniProtKB-KW.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR GO; GO:0008380; P:RNA splicing; IBA:GO_Central.
DR CDD; cd12324; RRM_RBM8; 1.
DR Gene3D; 3.30.70.330; -; 1.
DR InterPro; IPR012677; Nucleotide-bd_a/b_plait_sf.
DR InterPro; IPR035979; RBD_domain_sf.
DR InterPro; IPR008111; RNA-bd_8.
DR InterPro; IPR000504; RRM_dom.
DR InterPro; IPR033744; RRM_RBM8.
DR PANTHER; PTHR45894; PTHR45894; 1.
DR Pfam; PF00076; RRM_1; 1.
DR PRINTS; PR01738; RNABINDINGM8.
DR SMART; SM00360; RRM; 1.
DR SUPFAM; SSF54928; SSF54928; 1.
DR PROSITE; PS50102; RRM; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; mRNA processing; mRNA splicing; mRNA transport;
KW Nonsense-mediated mRNA decay; Nucleus; Reference proteome; RNA-binding;
KW Translation regulation; Transport.
FT CHAIN 1..197
FT /note="RNA-binding protein Y14B"
FT /id="PRO_0000440126"
FT DOMAIN 90..168
FT /note="RRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00176"
FT REGION 1..39
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 10..26
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 74
FT /note="A -> V (in Ref. 1; AHX83803)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 197 AA; 21969 MW; C6A754391149537D CRC64;
MAAAAEDVEF VDYDRDEEEE EDAMDEDDRG GGRGGRALPV PHIVSQGVMR SRGRLLGRST
SVLASNRDRF DSLADAGNPG HGPQRSIEGW ILLVSGVKED AEEDDLYNTF SDFGHVKDLH
LNLERRTGYA KGYALVEYES FEEAQTAIKA MNGTQLLTRT VYVDWAFSRG PIQKLTSTRP
LHRRSRTPPR RLAALTC
